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STRUCTURED HEALTH MARKUP LANGUAGE SHML ®

STRUCTURED HEALTH MARKUP LANGUAGE SHML ®. DAVID J. ROTHWELL M.D. HEALTH LANGUAGE CENTER. Major Issues Affecting Patient Medical Record Information. Continuing Barriers to Data Entry Increasing Role of Patient Choice Shift from Acute / Inpatient to Disease Prevention / Management

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STRUCTURED HEALTH MARKUP LANGUAGE SHML ®

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  1. STRUCTURED HEALTH MARKUP LANGUAGE SHML ® DAVID J. ROTHWELL M.D. HEALTH LANGUAGE CENTER

  2. Major Issues Affecting Patient Medical Record Information • Continuing Barriers to Data Entry • Increasing Role of Patient Choice • Shift from Acute / Inpatient to Disease Prevention / Management • Impact of Genomics • Rapid Rise of Internet Standards

  3. Health Language Center Approach • Convergence / Maturity of Two Major Technologies: • Internet Standards - XML • Natural Language Processing • Potential to Keep Pace with Change

  4. Care Process • Clinical Research • Aggregation of Data • Epidemiology • Adherence to guidelines • Eligibility for protocols PMRI Utility Provider Patient Document Findings PMRI NLP XML SHML • Clinically Important Information (minus) verbiage •  Clinically Relevant Content Units (CRCU) Text SDE

  5. Natural Language Processing • A system which turns natural language clinical documents into structured data for a variety of applications. • The NLP method makes explicit the informational structure of texts, using linguistic method and the most advanced information technology available today.

  6. NLP (cont’d) • Language presents information linearly in strings--phrases, sentences, paragraphs, sections, documents, discourses, … • Information in these strings is carried by the semantic types of words, occurring in particular combinations.

  7. Demographic Data Verbs Patient State Data Diagnosis S-S (H-INDIC) Patient Status Data Patient Anatomy (H-PTPART) Treatments Test and Result Time Uncertainty (H-MODAL) Negation Response Changes NLP Formats include:

  8. Use of Medical Language Processing for HEDIS Measures • "BETA BLOCKER TREATMENT AFTER A HEART ATTACK" • Hospital discharge -records in text form (natural language) are prepared • for processing, analyzed, formatted for retrieval of information, and the • following queries submitted by Aurum Medical Language Processor: •  Did the patient have an acute, myocardial infarction? •  Was the patient given a beta blocker medication? •  Did the patient have any contraindications?

  9. * List of Beta Blockers: LOPRESSOR, METOPROLOL, NADOLOL, • CORGARD, ATENOLOL, TENORMIN, PlNDOLOL, VISKEN, PROPRANOLOL, • INDERAL, INDURAL, BETA BLOCKER, ACEBUTOLOL, BETAXOLOL, • BISOPROLOL, CARTEOLOL, CARVEDLOL, LABETALOL, PENBUT0LOL, • SOTALOL, TIMOLOL. • * Listof Contraindications: HEART BLOCK, ATRIOVENTRICULAR BLOCK, • BRADYCARDIA, BRADYCARDIC, LV DYSFUNCTION, VENTRICULAR • DYSFUNCTION, DIASTOLIC DYSFUNCTION, VENTRICULAR DIASTOLIC • DYSFUNCTION, COPD, CHRONIC OBSTRUCTIVE PULMONARY DISEASE, • DIABETES MELLITUS, ASTHMA, CONGESTIVE HEART FAILURE, • * Results from database queries: • Beta Blocker Beta Blocker • Given Not Given TotalWith contraindications 42 19 61 Without contraindications28 2 30 Total 70 2l 91

  10. eXtensible Markup Language (XML) • Streamlined subset of SGML • XML is a language • Document Type Definition • DTD defines it's use (it's grammar) • Designed for data exchange • Data processing oriented rather than publishing (SGML) • Create own 'tags' -what you need to know • i.e. Annotate document with meaning

  11. eXtensible Markup Language (cont’d)(XML) • Data and document are combined • Tagged text transforms it into data • Tags are granular descriptive views of text • Tags are metadata--information not explicit in text • Puts meaning and interpretation on top of text • Ability to catalogue all information in document • Preserves fundamental structure of document (PMRI) • Tagged data can fit into any data format or data model

  12. XML Tags <elementType> Content </elementType> Pneumonia <Diagnosis> Pneumonia </Diagnosis> Pneumonia, right lower lobe <Diagnosis> Pneumonia <location> right lower lobe </location> </Diagnosis> Pneumonia, right lower lobe, superior, due to Klebsiella. <Diagnosis> Pneumonia <location> right lower lobe </location> <position> superior</position><link>due to</link> <org>Klebsiella </org> </Diagnosis> PRESENTATION FORMAT (one of many) Diagnosis: Pneumonia Location: RLL, superior Organism: Klebsiella

  13. XSL Demographic Data Node positive carcinoma of the left breast, treated by mastectomy, chemotherapy and radiotherapy Radiotherapy treatment summary: the left breast and draining nodal areas received a dose of 42.9 Gy in 13 fractions treating three times a week with 6 Mv photons. Treatment started on the 15th of September and was completed on the 14th October, 1995. Radiotherapy Treatment Summary Status before radiotherapy: Diagnosis Carcinoma left breast Spread Left axillary nodes Previous treatment Mastectomy, chemotherapy Radiotherapy given Treatment type 6 Mv photons Site Left chest wall and drainingnodes Total dose given 43 Gy Schedule 3 fractions/week 15 September 1995 to ... Follow up plan One visit . . .

  14. Structured Health Markup Language • Utilizes Linguistic Model not Coding • Utilizes XML • Designed to Integrate both Structured Data Entry and Text

  15. SHML® and MLP Medical documents MLP in HLC/SHML Dictionaries standardization Documents with SIDs • GENERATORS • SHML/DTD • SHML/XSL • SHML/XQL Documents in CRCU’s with SHML and MLP tags MLP Documents in rows of standard dBMS Other Applications

  16. Mapping --NLP Dictionary / SHML ® Term NLP Class SHML ® Altered awareness H-INDIC--N fs neuro Alternate H-TMREP--TV tmr Alternating between H-CONN--P lprep Altogether H-AMT--D mamt Aluminosis H-INDIC--N fd tox Augmentations H-CHANGE:MORE--N mcha August NTIME1--N tme Aunt H-FAMILY--N per kin Auricle H-PTPART--N as ear Auriculectomy H-TTCHIR--N pr Auriculo-osteodysplasia H-INDIC--N fd cong Auriculotemporal H-PTPART--ADJ areg Auscultate H-TXCLIN--TV pr

  17. SHML® TAGS Traditional Set • Demographic data <dem> (subclasses) • Anatomic Structure <A.S.> (Digital Anatomist) • Medication <dr> (Multum, First Data) • Organisms <or> • Chemical <ch> (nonphysiologic) • Devices <dev> (ECRI) • Occupation <occ> (National, international) • Procedures <pr> (CPT, other) • Diagnosis <fd> (ICD-9, ICD-O, Medcin)

  18. SHML ® TAGS (cont’d) Verbs <lv> Subsets defined by MLP Preposition <prep> All except time prep Dietary/Food <diet> Nutrition Time <tm> Exact, begin, end, frequency Amount <mamt> Change <mcha> Less, more Certainty <mcer> Uncertainty, modal, certainty Negation <mneg> Stage grade <ms-g> Dimension <mdim> Adjective <mad> Appearance <mapp> Color, shape, clarity Odor <msmell> Position <ppo> Top to bottom, laterality Person <per> Masc, Fem, pronouns Environment <env> Physical locations Transparent <transp> Derived from entity, modified

  19. Additional SHML ® TAGS Findings <Finding> Vital Signs Signs/symptoms by organ system Lab; Image; Behaviors Living Functional status Injury Disability Exposures Compliance Travel Dental ADL Alternative care Exercise etc. Leisure, sports Immunization Allergy, tolerances Education, counseling

  20. SHML ® / XML TAGGING<elementType>Content</elementType> Vocabulary Table Clinical Table Chest Pain Location Substernal Onset --hrs ago --days ago Brought on by jogging walking Relieved by rest nitroglycerin Terms Taxonomic knowledge Hierarchical knowledge (classificatory) Synonyms/Equivalent terms Linguistic knowledge Definitional knowledge Non-unique term knowledge Tag knowledge

  21. SHML Vocabulary Table (Outline) Digestive Tract (syn G.I. Tract, Alimentary Tract) Upper G.I. Tract Mouth Tongue Teeth Gums Pharynx Oropharynx Hypoharynx Esophagus Stomach Lower G.I. Tract Small Intestine Duodenum Jegunum Large Intestine Cecum Appendix Colon Rectum Anus

  22. Term/phraseRelation/Attribute Term/PhraseRelationRelation TAG (has member) Anatomic Structure as Integumentary System is a Anatomic StructureAnatomic Structure as Breast is a Anatomic StructureAnatomic Structure as Musculoskeletal System is a Anatomic StructureAnatomic Structure as Digestive System is a Anatomic StructureDigestive System as Digestive Tract is a Anatomic StructureDigestive System as Digestive Organs is a Anatomic StructureDigestive Tract as Upper GI Tract is a Anatomic StructureDigestive Tract as Lower GI Tract is a Anatomic Structure Upper G. I. Tract as Mouth is a Anatomic StructureOral syn Mouth BLANK BLANKUpper G. I. Tract as Pharynx is a Anatomic StructureUpper G. I. Tract as Esophagus is a Anatomic Structure Upper G. I. Tract as Stomach is a Anatomic Structure Mouth as Lips is a Anatomic StructureMouth as Tongue is a Anatomic Structure Mouth as Palate is a Anatomic StructureRoof of mouth syn Palate BLANK BLANK Tongue as Posterior third is a Anatomic StructureTongue as Anterior 2/3 is a AnatomicStructure

  23. Vocabulary Attribute Table Design---Findings Term/phrase Relation Term/phrase Relation Tag (has member) Finding is a Source Finding Finding Finding constitutional (fc) Finding Finding Finding tissue(ft) Finding Finding Finding integumentary (fs integ) Finding Finding Finding musculoskeletal (fsmss) Finding Finding Finding respiratory (fs resp) Finding Finding Finding neurologic (fs neuro) Finding neurological Finding Dyslexia is a Finding Finding neurological Finding Aphasia is a Finding Finding neurological Finding Phobia is a Finding Phobia Finding Acrophobia is a Finding Phobia Finding Claustrophobia is a Finding

  24. SHML® and NLP: Example #2 *SID=NE1519 017A.11.01 ON THE 16TH HOSPITAL DAY , AN ELECTROCARDIOGRAM SHOWED PROBABLE ATRIAL FIBRILLATION AT A VENTRICULAR RATE OF 100 , WITH PREMATURE VENTRICULAR CONTRACTIONS AND POSSIBLE OLD INFERIOR AND ANTEROSEPTAL MYOCARDIAL INFARCTS . WITH AND ON THE 16TH HOSPITAL DAY , AN ELECTRO-CARDIOGRAM SHOWED PROBABLE ATRIAL FIBRILLATION AT A VENTRICULAR RATE OF 100 AND PREMATURE VENTRICULAR CONTRACTIONS POSSIBLE OLD INFERIOR MYOCARDIAL INFARCTS POSSIBLE OLD ANTEROSEPTAL MYOCARDIAL INFARCTS

  25. SHML® and NLP: Example #2.1 *SID=NE1519 017A.11.01 ON THE 16TH HOSPITAL DAY , AN ELECTROCARDIOGRAM SHOWED PROBABLE ATRIAL FIBRILLATION AT A VENTRICULAR RATE OF 100 , WITH PREMATURE VENTRICULAR CONTRACTIONS AND POSSIBLE OLD INFERIOR AND ANTEROSEPTAL MYOCARDIAL INFARCTS . <CONNECTIVE><CONJOINED><CONN><P>WITH</P></CONN></CONJOINED> <PATIENT-STATE> <METHOD><PROCEDURE><T>AN</T><N><pr>ELECTROCARDIOGRAM</pr></N> </PROCEDURE></METHOD> <VERB><TV tense=“[PAST]”><show>SHOWED</show></TV> <EVENT-TIME><P>ON</P><T>THE </T><ADJ>16TH</ADJ> <N><env>HOSPITAL</env></N><N><tmloc>DAY</tmloc></N> , </EVENT-TIME></VERB> <PSTATE-DATA> <S-S><N><fns>FIBRILLATION</fns></N><P>AT</P> <MODS><MODAL><ADJ><mcer>PROBABLE</mcer></ADJ></MODAL> <PTPART><ADJ><ans>ATRIAL</ans></ADJ></PTPART></MODS></S-S> <PTFUNC><T>A</T><N><fun>RATE</fun></N><P>OF</P> <MODS><PTPART><ADJ><ans>VENTRICULAR</ans></ADJ></PTPART></MODS> </PTFUNC> <QUANT><Q-N><NUM><Q><numb>100</numb><Q>,</NUM></QN></QUANT></PSTATE-DATA> </PATIENT-STATE> next...

  26. SHML® and NLP: Example #2.2 *SID=NE1519 017A.11.01 ON THE 16TH HOSPITAL DAY , AN ELECTROCARDIOGRAM SHOWED PROBABLE ATRIAL FIBRILLATION AT A VENTRICULAR RATE OF 100 ,WITH PREMATUREVENTRICULAR CONTRACTIONS AND POSSIBLE OLD INFERIOR AND ANTEROSEPTAL MYOCARDIAL INFARCTS . WITH ON THE 16TH HOSPITAL DAY , AN ELECTROCARDIOGRAM SHOWED PROBABLE ATRIAL FIBRILLATION AT A VENTRICULAR RATE OF 100 <CONNECTIVE><CONJOINED><CONN>AND</CONN></CONJOINED> <PATIENT-STATE> <PSTATE-DATA> <S-S><ADJ><H-INDIC><tmloc>PREMATURE</tmloc></H-INDIC></ADJ></S-S> <PTPART><ADJ><H-PTPART><ans>VENTRICULAR</ans></H-PTPART></ADJ></PTPART> <PTFUNC><N><H-PTFUNC><fun>CONTRACTIONS</fun></H-PTFUNC></N></PTFUNC> </PSTATE-DATA> </PATIENT-STATE> next ...

  27. SHML® and NLP: Example #2.3 *SID=NE1519 017A.11.01 ON THE 16TH HOSPITAL DAY , AN ELECTROCARDIOGRAM SHOWED PROBABLE ATRIAL FIBRILLATION AT A VENTRICULAR RATE OF 100 ,WITH PREMATURE VENTRICULAR CONTRACTIONS AND POSSIBLE OLD INFERIOR AND ANTEROSEPTAL MYOCARDIAL INFARCTS . <CONNECTIVE><CONJOINED><CONN>AND</CONN></CONJOINED> <PATIENT-STATE><PSTATE-DATA> <DIAG><N><H-DIAG><ft>INFARCTS</ft></H-DIAG></N> <EVENT-TIME><ADJ><H-TMLOC><tmls>OLD</tmls></H-TMLOC></ADJ></EVENT-TIME> <MODS><MODAL><ADJ><H-MODAL><mcer>POSSIBLE</mcer></H-MODAL></ADJ> </MODAL><MODS></DIAG> <PTPART><ADJ><H-PTAREA><ppo>INFERIOR</ppo></H-PTAREA></ADJ> <ADJ><H-PTPART><as_cv>MYOCARDIAL</as_cv></H-PTPART></ADJ> </PTPART></PSTATE-DATA></PATIENT-STATE> <PATIENT-STATE><PSTATE-DATA> <DIAG><N><H-DIAG><ft>INFARCTS</ft></H-DIAG></N> <EVENT-TIME><ADJ><H-TMLOC><tmls>OLD</tmls></H-TMLOC></ADJ></EVENT-TIME> <MODS><MODAL><ADJ><H-MODAL><mcer>POSSIBLE</mcer></H-MODAL></ADJ> </MODAL><MODS></DIAG> <PTPART><ADJ><H-PTPART><ppo>ANTEROSEPTAL</ppo></H-PTPART></ADJ> <ADJ><H-PTPART><as_cv>MYOCARDIAL</as_cv></H-PTPART></ADJ> </PTPART></PSTATE-DATA></PATIENT-STATE> </CONNECTIVE></CONNECTIVE></CONNECTIVE>

  28. SHML® TAGGING

  29. Demographic Symptoms History Allergies 28 y/o female Stabbing, aching, burning pain, back of neck Pain radiating to right side into scapula Pain occurs occasional, usually end of day Numbness of left triceps occasional No urine problems No bowel problems No gait problems No drug allergies SHML® Tagging of Encounter

  30. SHML® Tagging (cont’d) Medications Physical Exam Impression Plan Advil, 400 mg.hs,prn Neck, normal position Neck supple Neck full range of motion Neck freedom of movement Right Trapezoid mildly tense Spine no point tenderness Arms, full strength Fingers, full strength Arms 1+ reflexes Legs 1+ reflexes Musculoskeletal pain Herniated disc, C-5 level, small symptoms mild Surgery not an option at this time MRI deferred until/should bowel findings bladder findings focal weakness (which persists) focal numbness (which persists) point tenderness(neck) Anvil 800 mg.tid, watch for G.I. side effects Physical therapy

  31. Potential of SHML® Approach • Ability to Resolve Ambiguity • Ability to Deal with Multiple Hierarchies

  32. NLP / SHML ® Depression <fs psy> psychological <ft> depression of surface, shape <mcha> depression of WBC, platelet “ST segment depression” - idiom (phrasal term)

  33. NLP / SHML ® EKG revealed sinus bradycardia <pr cv ekg> <show> <fs cv> <as cv> Heart <as resp> Repiratory <as mss> Within bone <ft> Rectal sinus, (fistula)

  34. Use with Structured Data Entry Chest Pain Onset # hrs ago # days ago Duration 20 min 1 day Location Laterality Character Brought on by Associated with Aggravated Relieved by Severity Radiating to Trend tmbeg tmd A.S. ppo-lat fi-SS- fac fi-SS li li mamt li fres

  35. Structured Health Markup LanguageSHML ® /XML • Adopt rules, notation that are in place for SGML/XML for the medical record (PMRI) • Create an architecture for data types • Structure the EMR • Utilize XML rules, notation for content (semantics) • eXtensible Markup Language (XML) • SHML/XML works with language; it does not reinvent it!!! • XML provides structure and contextual meaning to a document • XML is a self describing data structure

  36. STRUCTURED HEALTH MARKUP LANGUAGE SHML® • Subcomponent of XML • Health DTD for validation tags and their rendering • Tags assigned to terms/phrases and CRCUs • Tags specific for health • Tags specific for NLP • Structured • Defines a syntax of tags • Rules of well-formedness • XSL eXtensible Style Language for rendering

  37. SHML® vs MLP elementType’s • MLP (syntactic) part-of-speech elementType’s are based on major word classes, e.g. nouns (N), adjectives (ADJ), tensed verbs (TV), adverbs (D),… E.g. shortness of breath, <N>; • MLP co-occurrence semantic elementType’s are based on word usage (context), e.g. shortness ofbreath, <H-INDIC>; • SHML semantic elementType’s are based on medical knowledge (classification), e.g. shortnessof breath, <fs_resp>.

  38. SHML® DTD for CRCU’s <? XML VERSION=“1.0 ?> <!DOCTYPE STRUCTURED HEALTH MARKUP LANGUAGE “shml.dtd”> <!ELEMENT PATIENT-STATE (PARAGR, PT-DEMOG, METHOD, SUBJECT, VERB, TENSE, PSTATE-DATA, PRECISIONS, TIME, TEXTPLUS)> <!ELEMENT PATIENT-TREATMENTS (PARAGR, PT-DEMOG, TREATMENT, STATE-SUBJ, PRECISIONS, TIME, TEXTPLUS)> <!ELEMENT LABTEST (PARAGR,PT-DEMOG, INST, PT, TEST-INFO, VERB, TIME, TEXTPLUS)> <!ELEMENT PARAG (#PCDATA)*> <!ELEMENT PT-DEMOG (AGE, RACE, SEX, FAMILY)> <!ELEMENT AGE (#PCDATA)*> <!ELEMENT RACE (#PCDATA)*> <!ELEMENT SEX (MALE, FEMALE)> <!ELEMENT MALE (#PCDATA)*> <!ELEMENT FEMALE (#PCDATA)*> <!ELEMENT METHOD (PROCEDURE, EXAMTEST, DEVICE)> <!ELEMENT TREATMENT (GEN, CHIR, MED, COMP)> <!ELEMENT PROCEDURE (#PCDATA)*> <!ELEMENT EXAMTEST (#PCDATA)*> ...etc.

  39. Presentation of Data (Reformatting) • An echocardiogram performed in the Coronary Care Unit • shows dilated left atrium, moderate global LV dysfunction, • ejection fraction of 30%, moderate global RV dysfunction, • severe mitral regurgitation. • pr cv: Echocardiogram • Env (place): CCU • Finding cv: Dilated left atrium • Moderate global LV dysfunction • Ejection fraction 30% • Moderate global RV dysfunction • Severe mitral regurgitation

  40. Mission of HLC / SHML® • Define a granular representation of terms and phrases that within a given language (domain) unambiguously define clinical concepts • Provide for an adequate representation of these terms and concepts in a simple and easily understood architecture • Provide for discrete mapping to any other “nomenclature” and/or “code set” • Utilize easily available, inexpensive and widely supported tools for authoring, maintenance and use • Provide this as a non-proprietary standard under the auspices of a private not-for-profit entity

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